Opened 8 months ago
Closed 8 months ago
#17209 closed defect (can't reproduce)
RMSD header index error when restoring session
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> D:\TaxolManuscript\TaxolMTMap\StructuralFigure1\DimerRise\b3GDPvsTaxol.cxs
> format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 757, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 827, in restore_snapshot
inst._finalize_init(data['alignment'])
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 167, in _finalize_init
self.seq_canvas = SeqCanvas(parent, self, self.alignment)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 205, in __init__
self.layout_alignment()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 783, in layout_alignment
self.lead_block = SeqBlock(label_scene, self.main_scene, None, self.font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[Previous line repeated 83 more times]
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1645, in __init__
self.layout_lines(headers, self.header_label_color)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines
self._layout_line(line, label_color, bli, end)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line
item = self.make_item(line, self.seq_offset + i, xs[i],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2400, in make_item
info = line.depiction_val(offset)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
IndexError: list index out of range
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 757, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 827, in restore_snapshot
inst._finalize_init(data['alignment'])
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 167, in _finalize_init
self.seq_canvas = SeqCanvas(parent, self, self.alignment)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 205, in __init__
self.layout_alignment()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 783, in layout_alignment
self.lead_block = SeqBlock(label_scene, self.main_scene, None, self.font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[Previous line repeated 83 more times]
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1645, in __init__
self.layout_lines(headers, self.header_label_color)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines
self._layout_line(line, label_color, bli, end)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line
item = self.make_item(line, self.seq_offset + i, xs[i],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2400, in make_item
info = line.depiction_val(offset)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
IndexError: list index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest
self._callback(info)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\gui.py", line 423, in thread_safe
func(*args, **kw)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer
cxcmd(session, topic)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd
run(session, cmd)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 514, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 37, in open
return cxs_open(session, data, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 1027, in open
session.restore(stream, path=path, resize_window=resize_window,
combine=combine)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 765, in restore
self.reset()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset
sm.reset_state(container, self)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 273, in reset_state
alignment._destroy()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 724, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 471, in alignment_notification
self.delete()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 509, in delete
self.region_manager.destroy()
^^^^^^^^^^^^^^^^^^^
AttributeError: 'SequenceViewer' object has no attribute 'region_manager'
AttributeError: 'SequenceViewer' object has no attribute 'region_manager'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 509, in delete
self.region_manager.destroy()
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> open
> D:\TaxolManuscript\TaxolMTMap\StructuralFigure1\DimerRise\b3GDPvsTaxol.cxs
> format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 723, in restore
self.reset()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset
sm.reset_state(container, self)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 273, in reset_state
alignment._destroy()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 724, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 471, in alignment_notification
self.delete()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 509, in delete
self.region_manager.destroy()
^^^^^^^^^^^^^^^^^^^
AttributeError: 'SequenceViewer' object has no attribute 'region_manager'
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 723, in restore
self.reset()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset
sm.reset_state(container, self)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 273, in reset_state
alignment._destroy()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 724, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 471, in alignment_notification
self.delete()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 509, in delete
self.region_manager.destroy()
^^^^^^^^^^^^^^^^^^^
AttributeError: 'SequenceViewer' object has no attribute 'region_manager'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest
self._callback(info)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\gui.py", line 423, in thread_safe
func(*args, **kw)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer
cxcmd(session, topic)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd
run(session, cmd)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 514, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 37, in open
return cxs_open(session, data, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 1027, in open
session.restore(stream, path=path, resize_window=resize_window,
combine=combine)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 765, in restore
self.reset()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 552, in reset
sm.reset_state(container, self)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\manager.py", line 273, in reset_state
alignment._destroy()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 724, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 471, in alignment_notification
self.delete()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 509, in delete
self.region_manager.destroy()
^^^^^^^^^^^^^^^^^^^
AttributeError: 'SequenceViewer' object has no attribute 'region_manager'
AttributeError: 'SequenceViewer' object has no attribute 'region_manager'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 509, in delete
self.region_manager.destroy()
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> open
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDP-ChainH.pdb
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP D 41 ASP D 45 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1
3
Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1
3
Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1
8
53 messages similar to the above omitted
PDB SEQRES record for chain B is incomplete. Ignoring input sequence records
as basis for sequence.
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDP-ChainH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP D 41 GLN D 43 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1
3
Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1
3
Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1
8
245 messages similar to the above omitted
PDB SEQRES record for chain H is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for tsa_taxol_ChainB.pdb #1
---
Chain | Description
B | No description available
J | No description available
Chain information for tsaGDP-ChainH.pdb #2
---
Chain | Description
H | No description available
Associated tsa_taxol_ChainB.pdb chain J to tsa_taxol_ChainM-for_b3.pdb, chain
M with 0 mismatches
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 427, in <lambda>
self.associate([s for s in models if isinstance(s, AtomicStructure)],
force=False))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 394, in associate
self._notify_observers(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 482, in alignment_notification
self.seq_canvas.alignment_notification(note_name, note_data)
^^^^^^^^^^^^^^^
AttributeError: 'SequenceViewer' object has no attribute 'seq_canvas'
Error processing trigger "add models":
AttributeError: 'SequenceViewer' object has no attribute 'seq_canvas'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 482, in alignment_notification
self.seq_canvas.alignment_notification(note_name, note_data)
^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show "Color Actions"
> set bgColor white
> hide (protein|nucleic) target a
> cartoon hide
> show ((protein&@ca)|(nucleic&@p)) target ab
> size pseudobondRadius 0.3
Changed 3861 pseudobond radii
> ui tool show Matchmaker
> select #1/B:1-500, select #2/H:1-500
6673 atoms, 6823 bonds, 856 pseudobonds, 858 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #!2 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker tsa_taxol_ChainB.pdb, chain B (#1) with tsaGDP-ChainH.pdb, chain H
(#2), sequence alignment score = 1860.7
RMSD between 428 pruned atom pairs is 0.554 angstroms; (across all 429 pairs:
0.574)
> matchmaker #!2 & sel to #1 & sel showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker tsa_taxol_ChainB.pdb, chain B (#1) with tsaGDP-ChainH.pdb, chain H
(#2), sequence alignment score = 1860.7
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: tsa_taxol_ChainB.pdb #1/B,
tsaGDP-ChainH.pdb #2/H
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 428 pruned atom pairs is 0.554 angstroms; (across all 429 pairs:
0.574)
> sequence align 3 program muscle replace true
Webservices job id: IQNVBUXS55PN73LQ
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_rmsd #!1 target sabc palette 0,blue:0,white:8,red
16808 atoms, 2151 residues, atom seq_rmsd range 0.0502 to 58
C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py:1944: RuntimeWarning: invalid value
encountered in divide
color = numpy.sum(colors, axis=0) / len(colors)
C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py:1954: RuntimeWarning: invalid value
encountered in cast
brush = QBrush(QColor(*color.astype(int)), Qt.SolidPattern)
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
AttributeError: 'SeqBlock' object has no attribute 'next_block'
Error processing trigger "changes done":
AttributeError: 'SeqBlock' object has no attribute 'next_block'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
AttributeError: 'SeqBlock' object has no attribute 'next_block'
Error processing trigger "changes done":
AttributeError: 'SeqBlock' object has no attribute 'next_block'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
AttributeError: 'SeqBlock' object has no attribute 'next_block'
Error processing trigger "changes done":
AttributeError: 'SeqBlock' object has no attribute 'next_block'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color #2 #e5eaebff
> select clear
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
AttributeError: 'SeqBlock' object has no attribute 'next_block'
Error processing trigger "changes done":
AttributeError: 'SeqBlock' object has no attribute 'next_block'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
AttributeError: 'SeqBlock' object has no attribute 'next_block'
Error processing trigger "changes done":
AttributeError: 'SeqBlock' object has no attribute 'next_block'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.9126
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision 3540
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,985,317,376
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → RMSD header index error when restoring session |
comment:2 by , 8 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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